Equitation is judged on the rider, not the horse. Your position, handling of the horse, how you handle the questions asked in a jump course or flat class, etc. Hunt seat equitation is like hunters in the general style of riding (slightly in front of the vertical and similar basic positioning), but you will sit the canter in a flat class, unlike hunters where you will do whatever shows your horse off the best. I think equitation is a great division, but it sometimes encourages riders to focus on looking 'pretty' in the lower levels (which are fairly simple), not effective. It provides a solid foundation for riders to build upon, though.
Are you talking about IHSA for college riding? My trainer absolutely loved it and is a strong advocate of IHSA. She liked that fact that it is so welcoming to riders of all levels and gives riders so many opportunities and really levels the playing field as far as horses go. She won nationals in the open division twice and has told me numerous times that it helped her to manage her time because she was always either at the barn teaching or riding, or studying for school! She introduced me to Bob Cacchione, the founder of IHSA, down in Wellington this year and he's a really nice guy. All around it's just a great program.